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Riki Ohira, Hua Min, Larry Wright, Rick Kiefer, Troy Bleeker, Mike Riben, Grace Stafford, Stuart Turner, Sherri de Coronado

Review Items


See ORWG organizational maps including general view, provenance view, and subtopic/types view

OMV Core

Overall review of OMV core was completed by a small group on Wednesday 12 January 2011 (Stuart Bell, Sherri de Coronado, Rick Kiefer, Hua Min, Stuart Turner and Trish Whetzel). Comments are made on the OMV "Profile" metadata review page. There are some outstanding action items that require further research - we'll note their disposition on that page as well as in upcoming meetings. A summary of some of those items are listed below:

  1. Sherri and Stuart will review "Party", "Person", "Organization" and "Location" classes as part of the provenance review. Some of this relates to person (FOAF) and community (SIOC) metadata as well as resource identifiers (e.g. OID's)being reviewed by Grace.
  2. OntologyDomain
    1. To review candidate value set for repesentation of biomedical domains. Consider alignment with topic based structures or methods (e.g. DITA, Topic Maps, HL7 Infobutton, etc.)
      1. NLM's MeSH (Trish and others to review)
      2. NCI Thesaurus has created a list centered around occupations, disciplines, extramural affairs, other? To review this as a possible resource.
  3. OntologyTask
    1. OMV provides an enumerated list ("annotation", "configuration", "filtering", "indexing", "integration", "matching", "mediation", "query formulation", "query rewriting", 'personalization", "search"...). See pg 56 in OMV 2.4.1 specification.
      1. Review and advise on completeness and utility within our objectives
      2. Consider how task relates to description of ontology usage (as described in other models, such as CTS2)
  4. FormalityLevel
    1. Review OMV's enumeration ("catalog", "glossary", "thesauri", "taxonomy", "frames and properties", "value restrictions", "disjointness", "general logic constraints"). Consider refinement
      1. Evaluate list regarding classification of semantic precision and use in providing pre-built queries, views, etc.
  5. KnowledgeRepresentationParadigm
    1. e.g. "Description Logic", "Frames'
    2. Should this also be revised to describe if the paradigm represents the original source or was this derived or converted in a particular version/instance.
    3. Be sure community can clearly differentiate this from language and syntax
  6. OntologyLanguage
    1. e.g. "OWL", "OWL-DL", "OWL-Lite", "OWL-Full", "RDFs",
    2. Consider refinement (e.g. adding RRF)
    3. Review in context of CTS2
  7. OntologySyntax
    1. e.g. "OWL-XML", "RDF/XML", ec.
    2. Consider refinement for additional syntactical representation in the biomedical domain (e.g. OBO, LexGrid, etc.)
  8. OntologyEngineeringTool
    1. e.g. "Protege", "SWOOP", "TopQuadrant", "Altova Semantic Works", etc.
    2. Consider refinement (e.g. OBO Edit, NCI Protege, others)
  9. OntologyEngineering Methodology
    1. Definition and use of this is unclear. To seek better understanding by OMV developers (or others using it)
  10. LicenseModel
    1. Under review to clearly provide support (and understanding) for content vs. source code licensing. To evaluate context with "copyrights" and related properties in CTS2
  11. OntologyType
    1. e.g. "upper level", "core", "domain", "task", "application"
    2. Evaluate completeness and refinement as necessary
    3. Consider importance as a quality metric if a domain ontology was developed from an upper level ontology (e.g. BFO) for example

Other Representations - ISO 19763-3

  1. Under review by Hua. To present overall findings in an upcoming bi-weekly meeting (early February)
  2. Objectives
    1. Understand scope regarding machine and human readability (this standard appears directed to the former, not the latter)
    2. Understand functional scope (evolution and registration) and granularity of representation (changes to ontologies in whole or aggregate, class/property level, individuals, etc.)
    3. Understand real world examples or usage (it's a relatively nascent standard). Who's using this and how?
    4. Clearer understanding of functionality. Portions of published documentation remain unclear (some definitions are vague with circular reasoning for example)

Other Representations - CTS2

  1. CTS2 review, discussion week of 17 January 2011
  2. Present overall findings and recommendations within 4 weeks (week of 14 or 21 February)

Other Representations - Resource Identifiers

  1. Review recommendations for white paper regarding resource identifiers consistent with emerging standards, including SemWeb/W3C, CTS2, OWL 2, and especially OID's and registries within the biomedical domain (e.g. HL7, CDC, etc.)
  2. This work should be done cooperatively with CTS2 review


See ORWG organizational maps including general view, provenance view, and subtopic/types view

  1. Review community actors (entities and roles including persons and communities, groups, or projects) and metadata representation, especially both FOAF and SIOC.
  2. Repositories
    1. Clearly define (disambiguate) repository vs. registry vs. directory, as well as salient metadata representation (for example, OID's review by Grace)
      1. Review federation and notification methods
    2. Review relevant list of examples in biomedicine
      1. Trish to update group regarding groups out of Berkeley and MIT
  3. Community sub-group (Trish, Stuart B, Stuart T and others) to meet separately to review and prepare recommendations.
    1. Refine recommendations and write section for white paper
    2. Present findings with two-week period for review and commentary by group to ORWG biweekly meetings
      1. Present mid-February
      2. Feedback late-February

White paper

  • References (articles, other literature) can be posted to Basecamp due to fair use copyright restrictions (instead of the public wiki)
  • Will post BibTeX reference file. If others would prefer another format, let me know (~ Stuart)

Tentative Calendar

  • Posted on wiki and Basecamp
  • Writing sessions review weekly between 20 January - 14 March


  • ISO 19763-3 Review: 27 January 2011
  • Provenance Review: 10 February 2011
  • CTS2 Review: 24 February 2011
  • Collaboration Review. May require two sessions: Consider 3 & 10 March 2011
    • Modeling/Representation (metadata, etc.)
    • Repositories/Registries
    • Evaluation
      • Ranking, rating, trust, filtering
      • Explicit recommendation methods and sanctioning (e.g. certification)
    • Federation, services
    • Interactions/Discourse
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